Leaders from Catholic, Anglican, Presbyterian, Methodist and African Inland Churches all signed an open letter.
It urged their Muslim counterparts to directly tackle the Al Shabab terrorist group.
"We want to see a deliberate and concerted effort by our Muslim brothers and sisters.
"They [Muslim leaders] must move merely beyond condemning the spate of attacks targeting non-Muslims to initiating practical steps to the sympathisers of terror and helping us to build bridges between faiths and communities".
Al Shabab has killed hundreds of people in the past year including many Christians.
Last month an attack on a bus left 28 Christians dead whilst a mass shooting at a quarry killed 36.
"The attacks, which initially targeted Christian places of worship in Nairobi, Garissa and Mombasa, are now directly targeting innocent Christians in public transport and their places of work," the letter said.
"This year alone, over 20 attacks have been recorded in the country leaving behind a trail of death and destruction where over 200 Kenyans have lost their lives" the leaders recalled.
"The reality of this situation regrettably leads us to the conclusion that these attacks, perpetuated by people claiming to be Al Shabaab, are taking a religious angle".
Church leaders also urged Kenyans to "avoid statements that further incite and divide the Country along religious lines".